“Public health agencies are now able to harness the power of genome sequencing, which, when combined with the detailed clinical and epidemiological data we have access to, allows us to reconstruct outbreaks and really understand how a pathogen moves through a population,” says Jennifer Gardy of the British Columbia Center for Disease Control, presenting a case study where she and her colleagues used this new technique to track and eventually stop a tuberculosis outbreak in the province.

An outbreak of tuberculosis occurred over a 3-year period in a medium-sized community in British Columbia. In order to stop the event, public health officials turned to traditional epidemiological methods to identify the source and other contributing factors, but the results were hazy.

The researchers combined two new tools to get a clearer picture of the outbreak: social network analysis, which has become increasingly common in tracking infectious diseases in the past decade, and whole-genome sequencing (analysis of the entire microbe’s DNA), which has become cheaper and less time-consuming over the past few years.

“The complete genome sequence of a pathogen is the ultimate DNA fingerprint, and now, with the costs and time associated with genome sequencing dropping almost exponentially, it is possible to sequence most or all of the bacterial isolates taken from and outbreak,” says Gardy

And while it may sound like something having to do with Facebook, social network analysis takes traditional epidemiology one step further, asking patients about more than just with whom they have been in contact. In this case Gardy and her colleagues asked patients for a detailed account of their time on a daily basis including where they went and what they did at those places.

“Instead of getting a list of names, you are getting names, places and behaviors, and you can paint a much more detailed picture of the underlying structure. Key people and places and certain behaviors that might be contributing to an outbreak’s spread become much more apparent and allow you to adjust your outbreak investigation in real time as this new information becomes available,” says Gardy.

Using this new combinatorial technique, the researchers eventually determined that the outbreak was likely not instigated by genetic changes to the pathogen, but was instead likely due to increased usage of crack cocaine in the community. The disease was being transmitted in crack houses where people were coughing often while spending hours together in poorly ventilated rooms.

Additionally they were able to determine that a few key individuals acted as superspreaders, and these people were socially well connected and sympotmatic for long periods of time. This information is being used in a current outbreak investigation where public health officials are trying to target socially popular people for screening as a priority.

“We took an outbreak that was an absolute mystery by traditional methods and solved it using genome sequencing and social network analysis,” says Gardy who calls this and other genomic epidemiological studies “a new and exciting direction for epidemiology and the study of infectious disease, particularly for public health agencies.”

Source:
Jim Sliwa

American Society for Microbiology

In her research project, Baldwin and her colleagues will focus on establishing methods to identify potentially cancer-causing or other detrimental mutations in “induced pluripotent stem cells” (stem cells created from other cell types). Using cutting-edge whole genome sequencing methods, the laboratory will examine the source and scope of such mutations.

“Results of these studies will establish the relative safety of current methods to produce patient-matched reprogrammed cells and help to improve methods to speed the translation of these advances into therapies,” Baldwin said.

In his project, Gottesfeld and his collaborator Scripps Research Professor Jeanne Loring will use induced pluripotent stem cells to better understand a group of genetic diseases including Huntington’s disease, spinocerebella ataxias (a type of movement disorder), Myotonic Dystropy (a form of muscular dystrophy), Friedreich’s ataxia, and Fragile X syndrome. These inherited conditions are known as “triplet repeat” diseases because they are caused by abnormally repeated sequences of three nucleotides in an individual’s genetic code. Specifically, Gottesfeld and his colleagues will explore the molecular basis of the expansion/instability of triplet repeats that they have observed in stem cells from Friedreich’s ataxia patients.

“A fuller understanding of how repeats expand may lead to new drugs to treat these diseases,” noted Gottesfeld.

The grants to Scripps Research are part of the most recent round of CIRM funding, which included $37.7 million for Basic Biology Awards ($14.4 million of which was awarded to San Diego institutions), supporting research that leads to new insights in stem cell biology and disease origins.

Source:
Mika Ono
Scripps Research Institute

“Human Fetal Hemoglobin Expression is Regulated by the Developmental Stage-Specific Repressor BCL11A,” is published online in Science December 4. The study was conducted by researchers at Children’s Hospital Boston and Dana-Farber Cancer Institute and supported by the National Institutes of Health’s National Heart, Lung, and Blood Institute (NHLBI) and National Institutes of Diabetes and Digestive and Kidney Diseases, and by the Howard Hughes Medical Institute.

Hemoglobin is the protein in red blood cells that carries oxygen to the body’s tissues. In sickle cell disease, hemoglobin is abnormal and sticks together. The red blood cells become stiff and sickle-shaped, causing them to block blood vessels and rob tissues of necessary blood and oxygen. In thalassemia, the body has trouble producing adult forms of hemoglobin.

Other studies have shown that in patients with sickle cell disease, those who continue to produce fetal hemoglobin (HbF) have much milder forms of sickle cell anemia. For years, scientists have sought ways to increase HbF production in patients with sickle cell disease and thalassemia.

Researchers report that by suppressing a gene called BCL11A, HbF production improves dramatically. Their findings provide new insights into the mechanisms involved in the body’s switch from producing fetal hemoglobin to adult hemoglobin and identify a potential new target for therapies that could dramatically alter the course of sickle cell anemia and thalassemia.

The researchers built upon their recently reported results of genome-wide association studies that identified several gene variants associated with HbF levels. BCL11A was found to have the greatest effect on HbF levels. In the follow-up study reported today, they report that BCL11A encodes a transcription factor that directly suppresses HbF production.

A drug therapy that increases HbF levels enough to modify the severity of sickle cell disease is currently available. The drug hydroxyurea was approved by the FDA in 1998 to prevent pain crises in adults with sickle cell disease after studies showed that it increases fetal hemoglobin production, reduces the damaging effects of sickle cell disease, and improves some aspects of quality of life. Use of hydroxyurea is limited, however, in part because not all patients respond to the drug, and there are short-term and long-term adverse effects. New therapies targeting BCL11A would be the first to directly affect the natural processes involved in increasing HbF.

WHO: Alan Michelson, M.D., Ph.D., NHLBI associate director for basic research, and Susan Shurin, M.D., NHLBI deputy director and acting director of the NHLBI Division of Blood Diseases and Resources, are available to comment on these findings.

WHY: Sickle cell disease is the most common inherited blood disorder. In the United States, it affects approximately 70,000 people, primarily African Americans. Worldwide, sickle cell anemia affects millions of people and is found in people whose families come from Africa, South or Central America (especially Panama), Caribbean islands, Mediterranean countries, India, and Saudi Arabia.

The pain and complications associated with sickle cell disease can have a profound impact on patients’ quality of life, ability to work, and long-term health and well-being. In addition, people with sickle cell disease have a shortened life expectancy due to infections, lung problems, and stroke.

Treatments developed over the past three decades have led to the doubling of the life expectancy of sickle cell disease patients between 1972 and 2002. These treatments include medications, blood and bone marrow transfusions, and other procedures to relieve or prevent complications. Until now, however, scientists could not directly target processes known to affect the severity of sickle cell disease.

For more information:
NHLBI Announcement: Institute to Realign its Sickle Cell Disease Research Program, nhlbi.nih/meetings/workshops/Sickle-Cell-Announcement.htm

Sickle Cell Anemia, nhlbi.nih/health/dci/Diseases/Sca/SCA_WhatIs.html

Thalassemias, nhlbi.nih/health/dci/Diseases/Thalassemia/Thalassemia_WhatIs.html

NIH Consensus Development Conference: Hydroxyurea for Sickle Cell Disease, consensus.nih/2008/2008SickleCellCDC119main.htm

Part of the National Institutes of Health, the National Heart, Lung, and Blood Institute plans, conducts, and supports research related to the causes, prevention, diagnosis, and treatment of heart, blood vessel, lung, and blood diseases; and sleep disorders. The Institute also administers national health education campaigns on women and heart disease, healthy weight for children, and other topics. NHLBI press releases and other materials are available online at nhlbi.nih/.

The National Institutes of Health – The Nation’s Medical Research Agency – includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. It is the primary federal agency for conducting and supporting basic, clinical and translational medical research, and it investigates the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit nih.

Source: NHLBI Communications Office

NIH/National Heart, Lung and Blood Institute

Defective nucleoli have been implicated in several rare hereditary diseases, most recently also in neurodegenerative disorders such as Alzheimer’s and Huntington’s disease. Despite intense research efforts around the world, the molecular causes of Parkinson’s disease are still unclear. Under the leadership of Dr. Rosanna Parlato, scientists from the departments of Professor Dr. Guenther Schuetz and Professor Dr. Ingrid Grummt at DKFZ have investigated whether the demise of nucleoli also plays a role in this disease, which is also known as “shaking palsy”.

The investigators studied dopamine-producing neurons in the brain of Parkinson’s disease patients under the microscope. When Parkinson’s disease occurs, this type of cells malfunctions and dies, causing the characteristic palsy symptoms. Indeed, the majority of nucleoli in these cells were found to be defective.

This discovery caused the group to investigate whether disrupted nucleoli may really cause Parkinson’s-like symptoms or whether this was only an incidental finding. To this end, they modified the DNA of mice in such a way that the dopamine-producing cells of the experimental animals could only form defective nucleoli. These mice showed symptoms resembling Parkinson’s disease, such as characteristically impaired movements. In addition, the dopamine-producing neurons in their brain died prematurely.

In order to find out why these symptoms occur, the researchers took a closer look at all functions of the genetically modified cells. And they found an important change: The activity of the mTOR enzyme, a key regulator of intracellular signaling pathways, was reduced in the genetically modified cells. As a result of reduced mTOR activity, the function of mitochondria, the cellular power plants, is disrupted. This functional disruption causes oxidative stress within the cell; highly reactive oxygen compounds accumulate and cause damage to a multitude of molecules in the cell.

“Defective nucleoli apparently cause oxidative stress in cells. This can lead to massive cell damage and may be a key prerequisite for the typical nerve damage of Parkinson’s disease,” says Dr. Rosanna Parlato. “The dopamine-producing neurons are particularly sensitive to oxidative stress.” However, the scientists are not sure whether the damage in the nucleoli is really the sole cause of this neurodegeneration. “In any case, the nucleolus functions as a stress sensor showing us that a cell is in danger.”

Notes:

Claus Rieker, David Engblom, Grzegorz Kreiner, Andrii Domanskyi, Andreas Schober, Stefanie Stotz, Manuela Neumann, Xuejun Yuan, Ingrid Grummt, G??nther Sch??tz and Rosanna Parlato: Nucleolar Disruption in Dopaminergic Neurons Leads to Oxidative Damage and Parkinsonism through Repression of Mammalian Target of Rapamycin Signaling. The Journal of Neuroscience, January 12, 2011, 31(2):453-460, DOI:10.1523/JNEUROSCI.0590-10.2011

Source:
Dr. Sibylle Kohlstaedt

Helmholtz Association of German Research Centres

The researchers, led by Bevin Engelward, MIT associate professor of biological engineering, and Sangeeta Bhatia, professor in the Harvard-MIT Division of Health Sciences and Technology and MIT’s Department of Electrical Engineering and Computer Science, have produced a completely revamped version of a three-decades-old lab test known as the comet assay. This new technique combines the versatility and sensitivity of the comet assay for DNA damage analysis with a robust high-capacity platform, which could make DNA damage analysis routine across a variety of applications, ranging from epidemiology to drug screening.

Engelward, Bhatia, postdoctoral fellow David Wood and graduate student David Weingeist describe the technique in a paper that will appear in the Proceedings of the National Academy of Sciences the week of May 3.

The technology could offer a new approach for epidemiologists to detect dangerous environmental exposures long before they cause cancer, for clinicians to provide better cancer treatment, and for researchers in the pharmaceutical industry to identify new drugs and screen out hazardous drugs.

How they did it: The comet assay is based on the idea that during gel electrophoresis, a commonly used lab test in which an electric field is applied to DNA placed on a polymer gel, damaged DNA moves farther across the gel than undamaged DNA. The result is a “comet” made of DNA, which looks remarkably like its astronomical namesake. The assay is both sensitive and versatile, but it is also laborious and tedious. It requires at least one microscope slide for every experimental condition, which means that researchers need to juggle dozens of slides just to do a few experimental conditions. Additionally, the readout is entirely manual, meaning researchers have to spend hours staring into a microscope and selecting cells for analysis. The team’s goal was to harness the strengths of the comet assay while overcoming its limitations in throughput and labor.

Using a micopatterning technique developed by Wood and Bhatia, the research team imprinted a grid of tiny wells the size of a single cell on a DNA electrophoresis gel. Cells in the array can be individually “addressed,” which allows fully automated readout and replaces the tedious manual analysis. They also put their micoscopic cell array into a 96-well plate so that many cell types, drugs, or other conditions can be assayed simultaneously.

This setup allows dozens of experimental conditions to be tested on just one slide, and it enables slides to be automatically analyzed using custom-designed imaging software.

Next steps: The team is using knockout cell lines to determine which genetic deficiencies are detectable with their platform and to better understand the molecular mechanisms of DNA repair. They are also optimizing their system for human samples in order to study the DNA damaging effects of the environment. Ultimately, they hope that the CometChip will be commercialized and made available around the world. This technology was designed not only to enable high throughput screening, but also to be compatible with basic laboratory equipment so that virtually any laboratory can use it.

Notes:
“Single cell trapping and DNA damage analysis using microwell arrays,” Proceedings of the National Academy of Sciences, week of May 3. David Wood, David Weingeist, Sangeeta Bhatia and Bevin Engelward.

Source:
Jennifer Hirsch
Massachusetts Institute of Technology

The group, led by investigators from the School of Medicine at Cardiff in the United Kingdom and including scientists from Washington University School of Medicine in St. Louis, completed the largest genome-wide association study ever involving patients with Alzheimer’s disease. The study pooled DNA samples from more than 19,000 older European and U.S. residents. Seven thousand had Alzheimer’s disease, and the others had no clinical symptoms of the disorder.

Prior to this study, only four genes had been definitively associated with Alzheimer’s disease. Three genetic mutations have been identified as causes of rare, inherited forms of early-onset Alzheimer’s. The fourth gene, APOE4, is the only one previously linked to the more common late-onset form of the disease.

By looking at more than 600,000 common DNA markers, researchers on the current study were able to identify two new genes that appeared to be involved in elevated risk for Alzheimer’s and confirmed the importance of APOE4.

“There’s good evidence that these new genes may be novel risk factors, the first discovered since APOE in 1993,” says Washington University researcher and co-author Alison M. Goate, D.Phil. “So it’s a very important observation because this study is the first to provide such significant evidence of novel genetic risk factors for the most common form of Alzheimer’s disease.”

Goate, who in 1991 led a team in England that identified the first early-onset Alzheimer’s mutation in the APP gene on chromosome 21, is now the Samuel and Mae S. Ludwig Professor of Genetics in Psychiatry and professor of neurology at Washington University. She says the new genes identified in this study are APOJ, also called clustrin on chromosome 8, and PICALM on chromosome 11.

“The power of the new Genome Wide Association Study methods is that with large datasets we can now identify genes that earlier techniques were unable to confirm,” says co-author John C. Morris, M.D., of Washington University. “These new genes associated with Alzheimer’s disease provide new clues about how the illness develops.”

Morris, the Harvey A. and Dorismae Hacker Friedman Distinguished Professor of Neurology, is the director of Washington University’s Alzheimer’s Disease Research Center (ADRC). He says previous ADRC research suggests that in mice, the clustrin gene may be involved in the formation of amyloid deposits in the brain. Amyloid makes up the senile plaques that dot the brains of people with Alzheimer’s.

“These genes are both significant, but their effect appears to be much smaller than that of the APOE gene,” Goate says. “Using statistical methods, we’ve been able to estimate the amount of risk attributable to APOE at about 19 or 20 percent. The newly identified genes each come in under 10 percent, so it appears they have a much smaller effect.”

But not an insignificant one, Goate says, noting that although it isn’t yet clear how these new genes influence Alzheimer’s disease risk, levels of clustrin tend to rise when brain tissue is injured or becomes inflamed, and some researchers have noted increased clustrin levels in the brain and cerebrospinal fluid of Alzheimer’s patients.

The other gene, PICALM, appears to be involved in the breakdown of synapses, structures that allow neurons in the brain to communicate. Some scientists also hypothesize that the gene may be involved in the development of amyloid deposits, but Goate says much more work is required to identify exactly how PICALM elevates Alzheimer’s risk.

She expects many more genes also are involved in Alzheimer’s risk. In fact, this study identified 13 more gene variants worthy of further investigation.

The consortium of more than 80 scientists was led by Denise Harold, Ph.D., and Julie Williams, Ph.D., and their colleagues at Cardiff University. They used brain and blood tissues made available and analyzed by dozens of laboratories in the United Kingdom, Ireland, German, Belgium, Greece and the United States.

Harold D, et al. Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer’s disease. Nature Genetics, advance online publication. Sept. 6, 2009

This study was supported by several public and private funding agencies, including the Wellcome Trust and the National Institutes of Health. For a complete list of funders, please consult the acknowledgments section of the journal article.

Washington University School of Medicine’s 2,100 employed and volunteer faculty physicians also are the medical staff of Barnes-Jewish and St. Louis Children’s hospitals. The School of Medicine is one of the leading medical research, teaching and patient care institutions in the nation, currently ranked third in the nation by U.S. News & World Report. Through its affiliations with Barnes-Jewish and St. Louis Children’s hospitals, the School of Medicine is linked to BJC HealthCare.

Source
Washington University School of Medicine

These findings raise exciting questions, as EARTH explores in “Bacteria Back From the Brink” in the April issue. Could these hibernating microbes be brought back to active life today? If so, what can such microbes tell us about ancient life on Earth? And could similar microbes also be living on other planets?

Learn more about how these fascinating microbes stay alive over millennia, and read other stories on topics such as how black carbon affects climate, how to figure out if there is hexavalent chromium in your drinking water, and whether science education is passing or failing in the U.S. in the April issue.

Source:
Megan Sever

American Geological Institute

Wolfram Syndrome (WFS) is a rare, inherited neurodegenerative disorder. It is clinically heterogeneous, but it is primarily characterized by juvenile-onset diabetes mellitus, optic atrophy and premature death. Two different categories of WFS (WFS1 and 2) are recognized, each with its own subset of variable symptoms, and resulting from mutations in the WFS1 and CISD2 genes, respectively.

The CISD2 gene is located on the long arm of human chromosome number 4, which has been previously implicated in the regulation of human longevity through a comparative genome analysis of centenarian siblings. Dr. Tsai’s group sought to uncover the physiological function of CISD2.

The researchers engineered CISD2-deficient knock-out mice and, by 8 weeks old, observed an obvious premature-aging phenotype. The prematurely-aging CISD2-mutant mice displayed decreased body weight, shortened lifespan, and lower subcutaneous fat deposition, as well as clinical symptoms of WFS2 patients, including early-onset degeneration of optic, muscular and nervous tissues, and glucose sensitivity. Further study revealed that the Cisd2 protein is localized to the mitochondria, where it is required for proper mitochondrial structure and function.

This work establishes WFS2 as a mitochondrial-mediated disorder, whereby dysfunction in these cellular energy factories underlies muscle and neural cell degeneration, and accelerated ageing. Future work will examine the utility of this CISD2 mouse model to understand WFS2 pathogenesis, as well as explore the potential lifespan-extending effects of increased Cisd2 expression.

Source:
Heather Cosel-Pieper

Cold Spring Harbor Laboratory

The anthracycline class of chemotherapeutics – doxorubicin (Adriamycin), daunorubicin, epirubicin, idarubicin – have been used for four decades to treat many types of cancer, including leukemia, lymphoma, sarcomas and carcinomas, The standard method of administration had been to use the highest tolerable dose every few weeks to kill all rapidly growing cells by preventing them from accurately copying their genetic material.

“But the late Judah Folkman discovered in 2000 that so-called metronomic treatment, giving patients lower doses of these drugs more frequently, can keep cancer growth at bay by blocking blood vessel formation, but the exact mechanism by which this occurred wasn’t known,” says Gregg L. Semenza, M.D., Ph.D., director of the vascular program at the Johns Hopkins Institute for Cell Engineering and a member of the McKusick-Nathans Institute of Genetic Medicine. “Now we’ve shown how it happens and what players are involved, which could help shape future clinical trials for patients with certain types of cancers.”

Semenza and his team have long studied how the hypoxia-inducible factor, or HIF-1, protein helps cells survive under low-oxygen conditions. HIF-1 turns on genes that grow new blood vessels to help oxygen-starved cells, like those found in fast-growing solid tumors, survive.

To look for drugs that can prevent new blood vessel growth, the team tested more than 3,000 already FDA-approved drugs in the Johns Hopkins Drug Library for their ability to stop HIF-1 activity. Using modified liver cancer cells growing in low oxygen, the team treated cells with each of the drugs in the library and examined whether the drug could stop HIF-1 from turning on genes.

One drug – daunorubicin – reduced HIF-1′s gene-activating ability by more than 99 percent. They tested other members of the anthracycline drug class and found that doxorubicin, epirubicin and idarubicin also blocked HIF-1 activity. But further examination showed that both drug-treated and untreated cells contained similar amounts of HIF-1 protein, leading the researchers to conclude that the drugs are not affecting whether or not HIF-1 is made.

To turn on genes, HIF-1 must bind to DNA. So the research team looked at drug-treated and untreated cells and compared regions of DNA known to be bound by HIF-1. The sites that are bound by HIF-1 in untreated cells were found unbound in anthracycline treated cells. “We know that this class of drug prefers to bind to DNA sequences that are similar to the DNA sequence bound by HIF-1, but this is the first direct evidence that anthracyclines prevent HIF-1 from binding to and turning on target genes,” says Semenza.

To see if the interference with HIF-1 binding to DNA affects cancer growth, the team grew tumors in mice from human prostate cancer cells. They treated these mice with daunorubicin, doxorubicin or saline once a day for five days and measured tumor size. Tumors in saline-treated mice nearly doubled in size in that time, whereas tumors in the drug-treated mice stayed the same size or became smaller.

When the team examined the tumors from drug-treated mice, they found that the number of blood vessels was dramatically reduced compared to mice treated with saline. Additional tests revealed that the genes that HIF-1 turns on to drive blood vessel formation were turned off in tumors from the drug-treated mice.

“What this means, we hope, is that patients with a prostate cancer that has high HIF-1 levels – which puts them at greater risk of relapse following surgery or radiation therapy – might benefit from treatment with these drugs,” says Semenza. “However, clinical trials are necessary to determine whether this approach will help keep cancer patients alive.”

Authors of this paper are KangAe Lee, David Z. Qian, Sergio Rey, Hong Wei, Jun O. Liu and Gregg L. Semenza, all of Hopkins.

This work was funded by the Flight Attendant Medical Research Institute and the Johns Hopkins Institute for Cell Engineering.

On the Web:

hopkins-ice/index.html

hopkinsmedicine/geneticmedicine/

hopkinsmedicine/pharmacology/research/liu.html

pnas/

Source: Audrey Huang

Johns Hopkins Medical Institutions

The researchers of the IRIBHM have prooved, by the use of these genetically modified mice, that those abnormalities of B lymphocytes development and function are the result of an overexpression of molecule furthering apoptosis. The consequence of this overexpression is thus a decreased survival of the B lymphocytes and defect in antibody production in response to certain agents.

The IRIBHM’s team has also suggested a mechanism by which Inositol 1,3,4,5 tetrakisphosphate, the product generated by Itpkb, plays a significant role in the development and function of B lymphocytes : it controls the subcellular localization of the Rasa 3 enzyme, one of its intracellular receptors. Indeed, production of inositol 1,3,4,5-tetrakisphosphate in the cell results in the dissociation of the Rasa 3 receptor from the cell membrane and its inactivation.

This work follows other research still under way at the IRIBHM and focused on the unexpected but significant role of the Itpkb enzyme in T lymphocytes development. Considering the localization of the Itpkb gene in a region of the chromosom 1 known in man and mouse to contain several predisposition genes to autoimmune disease and considering this gene’s function in T and B lymphocytes development, the researchers of the IRIBHM investigate the hypothesis according to which alterations in this Itpkb gene could eventuallly favour the appearance of autoimmune disease (Disseminated Lupus Erythmatosus, type 1 diabetes,??¦).

This research, recently published in PNAS, has been done in collaboration with teams from the ULB (IRIBHM, IBMM), the Universite de Geneve, Harvard University and Bristol University.

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